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Someone by mistake ran latest dev and via singular...
# sarek_dev
e
Someone by mistake ran latest dev and via singularity multiqc bombed because 
multiqc
was not in the PATH in the image, is that expected?
m
what now?
definitively not expected
e
let me grab the log
Copy code
<pre><code>executor >  slurm (102)
[1d/fff7e3] NFC…MZ_v2_capture_targets.bed) | 1 of 1, cached: 1 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[54/b98fa3] NFC…T (chr1_11106506-11107529) | 1 of 1, cached: 1 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[38/8ca05e] NFC…cerBMZ_v2_capture_targets) | 1 of 1, cached: 1 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[69/910eaa] NFC…SAMTOOLS_STATS (B_6217996) | 14 of 14, cached: 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[06/181434] NFC…RECAL:MOSDEPTH (B_6217996) | 14 of 14, cached: 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[-        ] NFC…CHECKMATE:BCFTOOLS_MPILEUP -
[-        ] NFC…CHECKMATE:NGSCHECKMATE_NCM -
[d5/2a983d] NFC…APLOTYPECALLER (B_6205869) | 14 of 14, cached: 11 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[-        ] NFC…LLER:MERGE_HAPLOTYPECALLER -
[-        ] NFC…E_INDEX_SAMTOOLS:MERGE_BAM -
[-        ] NFC…X_SAMTOOLS:INDEX_MERGE_BAM -
[54/d51c1d] NFC…NSCOREVARIANTS (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[35/9879cc] NFC…ARIANTTRANCHES (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[a6/bc021b] NFC…BCFTOOLS_STATS (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[51/4f9cb6] NFC…OLS_TSTV_COUNT (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[18/4dcc9e] NFC…OOLS_TSTV_QUAL (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[92/819742] NFC…FTOOLS_SUMMARY (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[98/714c19] NFC…ENSEMBLVEP_VEP (B_6205869) | 14 of 14 <span class="emoji" style="font-family: 'Noto Color Emoji'">✔</span>
[7c/bc81ad] NFC…AREK:SAREK:MULTIQC (sarek) | 0 of 1 <span class="emoji" style="font-family: 'Noto Color Emoji'">✘</span>
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/sarek] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:MULTIQC (sarek)'

Caused by:
  Process `NFCORE_SAREK:SAREK:MULTIQC (sarek)` terminated with an error exit status (127)


Command executed:

  multiqc \
      --force \
       \
      --config 1/multiqc_config.yml \
       \
       \
       \
       \
      .

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 3: multiqc: command not found

Work dir:
  /home/incalci/shared/runs/OTH6_Butterfly/analysis/run1_targettato_PBMC_V350417070/sarek/work/7c/bc81adb4245ecc9350005f75385372

Container:
  /home/incalci/shared/singularity/community.wave.seqera.io-library-multiqc-1.35--839587b417d23042.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
I'm not sure what paths are expected, I thought some of ours might be shadowing them but it's not the case
r
What does the log say about which container it is using? If you pull the container manually are you able to reproduce this?
e
Yeah, I ran it manually, and it doesn't find multiqc on path (didn't pull though, I used the one we had already downloaded)
r
huh weird. because we don't see it in the CI tests confused dog https://github.com/nf-core/sarek/pull/2168
e
Just in case let me pull
m
That is super weird
I HAVE SEEN THE ERROR
I KNOW
.command.sh: line 12: samtools: command not found
ok, there might just be no samtools there
sorry
ok, very weird, I restarted the CI, and now samtools is in the container
confused dog
e
I had to go home yesterday, but a manual pull showed the correct command in path (????), I'll see about regenerating the image
Ok, regenerated, works. Truly a heisenbug....
💯 1
m
glad that this is not really an issue
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